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Chen Z, Choi ER, Encarnacion AM, Yao H, Ding M, Park YH, Choi SM, An YJ, Hong E, Choi HJ, Kim SK, Nam YE, Kim GJ, Park SW, Kim JS, Kim E, Lee S, Cho JH, Lee TH. Discovery of TCP-(MP)-caffeic acid analogs as a new class of agents for treatment of osteoclastic bone loss. Bioorg Chem 2024; 150:107603. [PMID: 38968905 DOI: 10.1016/j.bioorg.2024.107603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
Inhibition of LSD1 was proposed as promising and attractive therapies for treating osteoporosis. Here, we synthesized a series of novel TCP-(MP)-Caffeic acid analogs as potential LSD1 inhibitors to assess their inhibitory effects on osteoclastogenesis by using TRAP-staining assay and try to explore the preliminary SAR. Among them, TCP-MP-CA (11a) demonstrated osteoclastic bone loss both in vitro and in vivo, showing a significant improvement in the in vivo effects compared to the LSD1 inhibitor GSK-LSD1. Additionally, we elucidated a mechanism that 11a and its precursor that 11e directly bind to LSD1/CoREST complex through FAD to inhibit LSD1 demethylation activity and influence its downstream IκB/NF-κB signaling pathway, and thus regulate osteoclastic bone loss. These findings suggested 11a or 11e as potential novel candidates for treating osteoclastic bone loss, and a concept for further development of TCP-(MP)-Caffeic acid analogs for therapeutic use in osteoporosis clinics.
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Affiliation(s)
- Zhihao Chen
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Eun Rang Choi
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Alessandra Marie Encarnacion
- Department of Interdisciplinary Program of Biomedical Engineering, Graduate School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hongyuan Yao
- Department of Interdisciplinary Program of Biomedical Engineering, Graduate School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Mina Ding
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Young-Hoon Park
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Se Myeong Choi
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Yeon Jin An
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Hye-Ji Choi
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang Kyoon Kim
- Preclinical Research Center (PRC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea
| | - Ye Eun Nam
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang-Wook Park
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Eunae Kim
- Department of Pharmacy, College of Pharmacy, Chosun University, Gwangju 61452, Republic of Korea
| | - Sunwoo Lee
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jong Hyun Cho
- Department of Medicinal Biotechnology, College of Health Sciences, Dong-A University, Busan 49315, Republic of Korea; Department of Translational Biomedical Sciences, Graduate School of Dong-A University, Busan 49201, Republic of Korea.
| | - Tae-Hoon Lee
- Department of Oral Biochemistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea; Department of Interdisciplinary Program of Biomedical Engineering, Graduate School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea.
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2
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Cai W, Xiao C, Fan T, Deng Z, Wang D, Liu Y, Li C, He J. Targeting LSD1 in cancer: Molecular elucidation and recent advances. Cancer Lett 2024; 598:217093. [PMID: 38969160 DOI: 10.1016/j.canlet.2024.217093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/18/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
Histones are the main components of chromatin, functioning as an instructive scaffold to maintain chromosome structure and regulate gene expression. The dysregulation of histone modification is associated with various pathological processes, especially cancer initiation and development, and histone methylation plays a critical role. However, the specific mechanisms and potential therapeutic targets of histone methylation in cancer are not elucidated. Lys-specific demethylase 1A (LSD1) was the first identified demethylase that specifically removes methyl groups from histone 3 at lysine 4 or lysine 9, acting as a repressor or activator of gene expression. Recent studies have shown that LSD1 promotes cancer progression in multiple epigenetic regulation or non-epigenetic manners. Notably, LSD1 dysfunction is correlated with repressive cancer immunity. Many LSD1 inhibitors have been developed and clinical trials are exploring their efficacy in monotherapy, or combined with other therapies. In this review, we summarize the oncogenic mechanisms of LSD1 and the current applications of LSD1 inhibitors. We highlight that LSD1 is a promising target for cancer treatment. This review will provide the latest theoretical references for further understanding the research progress of oncology and epigenetics, deepening the updated appreciation of epigenetics in cancer.
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Affiliation(s)
- Wenpeng Cai
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chu Xiao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tao Fan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ziqin Deng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Di Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yixiao Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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3
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Liu TA, Stewart TM, Casero RA. The Synergistic Benefit of Combination Strategies Targeting Tumor Cell Polyamine Homeostasis. Int J Mol Sci 2024; 25:8173. [PMID: 39125742 PMCID: PMC11311409 DOI: 10.3390/ijms25158173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Mammalian polyamines, including putrescine, spermidine, and spermine, are positively charged amines that are essential for all living cells including neoplastic cells. An increasing understanding of polyamine metabolism, its molecular functions, and its role in cancer has led to the interest in targeting polyamine metabolism as an anticancer strategy, as the metabolism of polyamines is frequently dysregulated in neoplastic disease. In addition, due to compensatory mechanisms, combination therapies are clinically more promising, as agents can work synergistically to achieve an effect beyond that of each strategy as a single agent. In this article, the nature of polyamines, their association with carcinogenesis, and the potential use of targeting polyamine metabolism in treating and preventing cancer as well as combination therapies are described. The goal is to review the latest strategies for targeting polyamine metabolism, highlighting new avenues for exploiting aberrant polyamine homeostasis for anticancer therapy and the mechanisms behind them.
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Affiliation(s)
- Ting-Ann Liu
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA;
| | - Tracy Murray Stewart
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA;
| | - Robert A. Casero
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA;
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Zhao T, Hong Y, Yan B, Huang S, Ming GL, Song H. Epigenetic maintenance of adult neural stem cell quiescence in the mouse hippocampus via Setd1a. Nat Commun 2024; 15:5674. [PMID: 38971831 PMCID: PMC11227589 DOI: 10.1038/s41467-024-50010-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/25/2024] [Indexed: 07/08/2024] Open
Abstract
Quiescence, a hallmark of adult neural stem cells (NSCs), is required for maintaining the NSC pool to support life-long continuous neurogenesis in the adult dentate gyrus (DG). Whether long-lasting epigenetic modifications maintain NSC quiescence over the long term in the adult DG is not well-understood. Here we show that mice with haploinsufficiency of Setd1a, a schizophrenia risk gene encoding a histone H3K4 methyltransferase, develop an enlarged DG with more dentate granule cells after young adulthood. Deletion of Setd1a specifically in quiescent NSCs in the adult DG promotes their activation and neurogenesis, which is countered by inhibition of the histone demethylase LSD1. Mechanistically, RNA-sequencing and CUT & RUN analyses of cultured quiescent adult NSCs reveal Setd1a deletion-induced transcriptional changes and many Setd1a targets, among which down-regulation of Bhlhe40 promotes quiescent NSC activation in the adult DG in vivo. Together, our study reveals a Setd1a-dependent epigenetic mechanism that sustains NSC quiescence in the adult DG.
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Affiliation(s)
- Ting Zhao
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA
| | - Yan Hong
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA
| | - Bowen Yan
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Suming Huang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philedaphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Jasmine S, Mandl A, Krueger TEG, Dalrymple SL, Antony L, Dias J, Celatka CA, Tapper AE, Kleppe M, Kanayama M, Jing Y, Speranzini V, Wang YZ, Luo J, Trock BJ, Denmeade SR, Carducci MA, Mattevi A, Rienhoff HY, Isaacs JT, Brennen WN. Characterization of structural, biochemical, pharmacokinetic, and pharmacodynamic properties of the LSD1 inhibitor bomedemstat in preclinical models. Prostate 2024; 84:909-921. [PMID: 38619005 PMCID: PMC11184632 DOI: 10.1002/pros.24707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
INTRODUCTION Lysine-specific demethylase 1 (LSD1) is emerging as a critical mediator of tumor progression in metastatic castration-resistant prostate cancer (mCRPC). Neuroendocrine prostate cancer (NEPC) is increasingly recognized as an adaptive mechanism of resistance in mCRPC patients failing androgen receptor axis-targeted therapies. Safe and effective LSD1 inhibitors are necessary to determine antitumor response in prostate cancer models. For this reason, we characterize the LSD1 inhibitor bomedemstat to assess its clinical potential in NEPC as well as other mCRPC pathological subtypes. METHODS Bomedemstat was characterized via crystallization, flavine adenine dinucleotide spectrophotometry, and enzyme kinetics. On-target effects were assessed in relevant prostate cancer cell models by measuring proliferation and H3K4 methylation using western blot analysis. In vivo, pharmacokinetic (PK) and pharmacodynamic (PD) profiles of bomedemstat are also described. RESULTS Structural, biochemical, and PK/PD properties of bomedemstat, an irreversible, orally-bioavailable inhibitor of LSD1 are reported. Our data demonstrate bomedemstat has >2500-fold greater specificity for LSD1 over monoamine oxidase (MAO)-A and -B. Bomedemstat also demonstrates activity against several models of advanced CRPC, including NEPC patient-derived xenografts. Significant intra-tumoral accumulation of orally-administered bomedemstat is measured with micromolar levels achieved in vivo (1.2 ± 0.45 µM at the 7.5 mg/kg dose and 3.76 ± 0.43 µM at the 15 mg/kg dose). Daily oral dosing of bomedemstat at 40 mg/kg/day is well-tolerated, with on-target thrombocytopenia observed that is rapidly reversible following treatment cessation. CONCLUSIONS Bomedemstat provides enhanced specificity against LSD1, as revealed by structural and biochemical data. PK/PD data display an overall safety profile with manageable side effects resulting from LSD1 inhibition using bomedemstat in preclinical models. Altogether, our results support clinical testing of bomedemstat in the setting of mCRPC.
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Affiliation(s)
- Sumer Jasmine
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adel Mandl
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Timothy E. G. Krueger
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Susan L. Dalrymple
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lizamma Antony
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer Dias
- Imago Biosciences Inc., A Subsidiary of Merck & Co, Inc., San Francisco, California, USA
| | - Cassandra A. Celatka
- Imago Biosciences Inc., A Subsidiary of Merck & Co, Inc., San Francisco, California, USA
| | - Amy E. Tapper
- Imago Biosciences Inc., A Subsidiary of Merck & Co, Inc., San Francisco, California, USA
| | - Maria Kleppe
- Imago Biosciences Inc., A Subsidiary of Merck & Co, Inc., San Francisco, California, USA
| | - Mayuko Kanayama
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yuezhou Jing
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Yuzhuo Z. Wang
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Experimental Therapeutics, Vancouver Prostate Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Jun Luo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bruce J. Trock
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Samuel R. Denmeade
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael A. Carducci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Hugh Y. Rienhoff
- Imago Biosciences Inc., A Subsidiary of Merck & Co, Inc., San Francisco, California, USA
| | - John T. Isaacs
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - W. Nathaniel Brennen
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Zhang Y, Du Y, Liao K, Peng T. Modular development of organelle-targeting fluorescent probes for imaging formaldehyde in live cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3646-3653. [PMID: 38738568 DOI: 10.1039/d4ay00360h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Formaldehyde (FA) is endogenously generated via fundamental biological processes in living systems. Aberrant FA homeostasis in subcellular microenvironments is implicated in numerous pathological conditions. Fluorescent probes for detecting FA in specific organelles are thus of great research interest. Herein, we present a modular strategy to construct diverse organelle-targeting FA probes by incorporating selective organelle-targeting moieties into the scaffold of a 1,8-naphthalimide-derived FA fluorescent probe. These probes react with FA through the 2-aza-Cope arrangement and exhibit highly selective fluorescence increases for detecting FA in aqueous solutions. Moreover, these organelle-targeting probes, i.e., FFP551-Nuc, FFP551-ER, FFP551-Mito, and FFP551-Lyso, allow selective localization and imaging of FA in the nucleus, endoplasmic reticulum, mitochondria, and lysosomes of live mammalian cells, respectively. Furthermore, FFP551-Nuc has been successfully employed to monitor changes of endogenous FA levels in the nucleus of live mammalian cells. Overall, these probes should represent new imaging tools for studying the biology and pathology associated with FA in different intracellular compartments.
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Affiliation(s)
- Yuqing Zhang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Yimeng Du
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Kongke Liao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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Kim HM, Liu Z. LSD2 Is an Epigenetic Player in Multiple Types of Cancer and Beyond. Biomolecules 2024; 14:553. [PMID: 38785960 PMCID: PMC11118440 DOI: 10.3390/biom14050553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Histone demethylases, enzymes responsible for removing methyl groups from histone proteins, have emerged as critical players in regulating gene expression and chromatin dynamics, thereby influencing various cellular processes. LSD2 and LSD1 have attracted considerable interest among these demethylases because of their associations with cancer. However, while LSD1 has received significant attention, LSD2 has not been recognized to the same extent. In this study, we conduct a comprehensive comparison between LSD2 and LSD1, with a focus on exploring LSD2's implications. While both share structural similarities, LSD2 possesses unique features as well. Functionally, LSD2 shows diverse roles, particularly in cancer, with tissue-dependent roles. Additionally, LSD2 extends beyond histone demethylation, impacting DNA methylation, cancer cell reprogramming, E3 ubiquitin ligase activity and DNA damage repair pathways. This study underscores the distinct roles of LSD2, providing insights into their contributions to cancer and other cellular processes.
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Affiliation(s)
- Hyun-Min Kim
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan 215316, China
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Han D, Lu J, Fan B, Lu W, Xue Y, Wang M, Liu T, Cui S, Gao Q, Duan Y, Xu Y. Lysine-Specific Demethylase 1 Inhibitors: A Comprehensive Review Utilizing Computer-Aided Drug Design Technologies. Molecules 2024; 29:550. [PMID: 38276629 PMCID: PMC10821146 DOI: 10.3390/molecules29020550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) has emerged as a promising therapeutic target for treating various cancers (such as breast cancer, liver cancer, etc.) and other diseases (blood diseases, cardiovascular diseases, etc.), owing to its observed overexpression, thereby presenting significant opportunities in drug development. Since its discovery in 2004, extensive research has been conducted on LSD1 inhibitors, with notable contributions from computational approaches. This review systematically summarizes LSD1 inhibitors investigated through computer-aided drug design (CADD) technologies since 2010, showcasing a diverse range of chemical scaffolds, including phenelzine derivatives, tranylcypromine (abbreviated as TCP or 2-PCPA) derivatives, nitrogen-containing heterocyclic (pyridine, pyrimidine, azole, thieno[3,2-b]pyrrole, indole, quinoline and benzoxazole) derivatives, natural products (including sanguinarine, phenolic compounds and resveratrol derivatives, flavonoids and other natural products) and others (including thiourea compounds, Fenoldopam and Raloxifene, (4-cyanophenyl)glycine derivatives, propargylamine and benzohydrazide derivatives and inhibitors discovered through AI techniques). Computational techniques, such as virtual screening, molecular docking and 3D-QSAR models, have played a pivotal role in elucidating the interactions between these inhibitors and LSD1. Moreover, the integration of cutting-edge technologies such as artificial intelligence holds promise in facilitating the discovery of novel LSD1 inhibitors. The comprehensive insights presented in this review aim to provide valuable information for advancing further research on LSD1 inhibitors.
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Affiliation(s)
- Di Han
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Jiarui Lu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Baoyi Fan
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Wenfeng Lu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yiwei Xue
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Meiting Wang
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Taigang Liu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Shaoli Cui
- School of Forensic, Xinxiang Medical University, Xinxiang 453003, China
| | - Qinghe Gao
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China
| | - Yingchao Duan
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China
| | - Yongtao Xu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (D.H.); (J.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
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Takada Y, Adachi K, Fujinaga Y, Yamashita Y, Itoh Y, Suzuki T. A Structure-Activity Relationship Study of SNAIL1 Peptides as Inhibitors of Lysine-Specific Demethylase 1. Chem Pharm Bull (Tokyo) 2024; 72:155-160. [PMID: 38296557 DOI: 10.1248/cpb.c23-00671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Peptides have recently garnered attention as middle-molecular-weight drugs with the characteristics of small molecules and macromolecules. Lysine-specific demethylase 1 (LSD1) is a potential therapeutic target for lung cancer, neuroblastoma, and leukemia, and some peptide-based LSD1 inhibitors designed based on the N-terminus of SNAIL1, a member of the SNAIL/SCRATCH family of transcription factors, have been reported. The N-terminus of SNAIL1 peptide acts as a cap of the catalytic site of LSD1, inhibiting interactions with LSD1. However, the structure-activity relationship (SAR) of these inhibitors is not yet fully understood. Therefore, in the present study, we aimed to uncover the SAR and to identify novel SNAIL1 peptide-based LSD1 inhibitors. We synthesized peptide inhibitor candidates based on truncating the N-terminus of SNAIL1 or substituting its amino acid residues. In the truncation study, we found that SNAIL1 1-16 (2), which was composed of 16 residues, strongly inhibited LSD1. Furthermore, we investigated the SAR at residues-3 and -5 from the N-terminus and found that peptides 2j and 2k, in which leucine 5 of the parent peptide is substituted with unnatural amino acids, cyclohexylalanine and norleucine, respectively, strongly inhibited LSD1. This result suggests that the hydrophobic interaction between the inhibitor peptides and LSD1 affects the LSD1-inhibitory activity. We believe that this SAR information provides a basis for the development of more potent LSD1 inhibitors.
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10
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Chen D, Chen S, Zhou F, Bo Chen L, Chen MW. Synergistic Effects of Tranylcypromine and NRF2 Inhibitor: A Repurposing Strategy for Effective Cancer Therapy. ChemMedChem 2023; 18:e202300282. [PMID: 37871186 DOI: 10.1002/cmdc.202300282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Drug repurposing has emerged as an attractive strategy for accelerating drug discovery for cancer treatment. In this study, we investigated combining Tranylcypromine (TCP) with a number of well-characterized drugs. Among these combinations, NRF2 inhibitor (ML385) exhibited synergistic effects in combination with TCP. Specifically, our results showed that the combination of TCP and ML385 resulted in a significant reduction in tumor proliferation while neither drug affected cancer cell growth meaningfully on its own. While further studies are needed to understand fully the extent of the synergistic efficacy, the underlying respective mechanisms and the potential side effects of this approach, our study has yielded a promising start for the development of an effective combination cancer therapy.
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Affiliation(s)
- Delos Chen
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
- Mustians House, Eton College, Eton Wick Road, SL4 6EX, Eton, Berkshire, UK
| | - Skye Chen
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
- Mustians House, Eton College, Eton Wick Road, SL4 6EX, Eton, Berkshire, UK
| | - Fangheng Zhou
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
| | - Lan Bo Chen
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
- Department of Pathology, Harvard Medical School, 25 Shattuck Street, 02115, Boston, MA, USA
| | - Ming-Wei Chen
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
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11
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Azargoonjahromi A. The role of epigenetics in anxiety disorders. Mol Biol Rep 2023; 50:9625-9636. [PMID: 37804465 DOI: 10.1007/s11033-023-08787-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/30/2023] [Indexed: 10/09/2023]
Abstract
Anxiety disorders (ADs) are extremely common psychiatric conditions that frequently co-occur with other physical and mental disorders. The pathophysiology of ADs is multifaceted and involves intricate connections among biological elements, environmental stimuli, and psychological mechanisms. Recent discoveries have highlighted the significance of epigenetics in bridging the gap between multiple risk factors that contribute to ADs and expanding our understanding of the pathomechanisms underlying ADs. Epigenetics is the study of how changes in the environment and behavior can have an impact on gene function. Indeed, researchers have found that epigenetic mechanisms can affect how genes are activated or inactivated, as well as whether they are expressed. Such mechanisms may also affect how ADs form and are protected. That is, the bulk of pharmacological trials evaluating epigenetic treatments for the treatment of ADs have used histone deacetylase inhibitors (HDACi), yielding promising outcomes in both preclinical and clinical studies. This review will provide an outline of how epigenetic pathways can be used to treat ADs or lessen their risk. It will also present the findings from preclinical and clinical trials that are currently available on the use of epigenetic drugs to treat ADs.
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12
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Baby S, Shinde SD, Kulkarni N, Sahu B. Lysine-Specific Demethylase 1 (LSD1) Inhibitors: Peptides as an Emerging Class of Therapeutics. ACS Chem Biol 2023; 18:2144-2155. [PMID: 37812385 DOI: 10.1021/acschembio.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Aberrant expression of the epigenetic regulator lysine-specific demethylase 1 (LSD1) has been associated with the incidence of many diseases, particularly cancer, and it has evolved as a promising epigenetic target over the years for treatment. The advent of LSD1 inhibitor-based clinical utility began with tranylcypromine, and it is now considered an inevitable scaffold in the search for other irreversible novel LSD1 inhibitors (IMG-7289 or bomedemstat, ORY1001 or iadademstat, ORY-2001 or vafidemstat, GSK2879552, and INCB059872). Moreover, numerous reversible inhibitors for LSD1 have been reported in the literature, including clinical candidates CC-90011 (pulrodemstat) and SP-2577 (seclidemstat). There is parallel mining for peptide-based LSD1 inhibitors, which exploits the opportunities in the LSD1 substrate binding pocket. This Review highlights the research progress on reversible and irreversible peptide/peptide-derived LSD1 inhibitors. For the first time, we comprehensively organized the peptide-based LSD1 inhibitors from the design strategy. Peptide inhibitors of LSD1 are classified as H3 peptide and SNAIL1 peptide derivatives, along with miscellaneous peptides that include naturally occurring LSD1 inhibitors.
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Affiliation(s)
- Stephin Baby
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Suchita Dattatray Shinde
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Neeraj Kulkarni
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
| | - Bichismita Sahu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India
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13
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Lu CF, Zhou YN, Zhang J, Su S, Liu Y, Peng GH, Zang W, Cao J. The role of epigenetic methylation/demethylation in the regulation of retinal photoreceptors. Front Cell Dev Biol 2023; 11:1149132. [PMID: 37305686 PMCID: PMC10251769 DOI: 10.3389/fcell.2023.1149132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Photoreceptors are integral and crucial for the retina, as they convert light into electrical signals. Epigenetics plays a vital role in determining the precise expression of genetic information in space and time during the development and maturation of photoreceptors, cell differentiation, degeneration, death, and various pathological processes. Epigenetic regulation has three main manifestations: histone modification, DNA methylation, and RNA-based mechanisms, where methylation is involved in two regulatory mechanisms-histone methylation and DNA methylation. DNA methylation is the most studied form of epigenetic modification, while histone methylation is a relatively stable regulatory mechanism. Evidence suggests that normal methylation regulation is essential for the growth and development of photoreceptors and the maintenance of their functions, while abnormal methylation can lead to many pathological forms of photoreceptors. However, the role of methylation/demethylation in regulating retinal photoreceptors remains unclear. Therefore, this study aims to review the role of methylation/demethylation in regulating photoreceptors in various physiological and pathological situations and discuss the underlying mechanisms involved. Given the critical role of epigenetic regulation in gene expression and cellular differentiation, investigating the specific molecular mechanisms underlying these processes in photoreceptors may provide valuable insights into the pathogenesis of retinal diseases. Moreover, understanding these mechanisms could lead to the development of novel therapies that target the epigenetic machinery, thereby promoting the maintenance of retinal function throughout an individual's lifespan.
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Affiliation(s)
- Chao-Fan Lu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Ya-Nan Zhou
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jingjing Zhang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Songxue Su
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Yupeng Liu
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Guang-Hua Peng
- Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou, China
- Laboratory of Visual Cell Differentiation and Regulation, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Weidong Zang
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
| | - Jing Cao
- Department of Anatomy, Basic Medical College, Zhengzhou University, Zhengzhou, China
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14
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Bales KL, Hang S, Paulus JP, Jahanfard E, Manca C, Jost G, Boyer C, Bern R, Yerumyan D, Rogers S, Mederos SL. Individual differences in social homeostasis. Front Behav Neurosci 2023; 17:1068609. [PMID: 36969803 PMCID: PMC10036751 DOI: 10.3389/fnbeh.2023.1068609] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/15/2023] [Indexed: 03/12/2023] Open
Abstract
The concept of “social homeostasis”, introduced by Matthews and Tye in 2019, has provided a framework with which to consider our changing individual needs for social interaction, and the neurobiology underlying this system. This model was conceived as including detector systems, a control center with a setpoint, and effectors which allow us to seek out or avoid additional social contact. In this article, we review and theorize about the many different factors that might contribute to the setpoint of a person or animal, including individual, social, cultural, and other environmental factors. We conclude with a consideration of the empirical challenges of this exciting new model.
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Affiliation(s)
- Karen L. Bales
- Department of Psychology, University of California, Davis, >Davis, CA, United States
- *Correspondence: Karen L. Bales
| | - Sally Hang
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - John P. Paulus
- Graduate Group in Neuroscience, University of California, Davis, Davis, CA, United States
| | - Elaina Jahanfard
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Claudia Manca
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Geneva Jost
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Chase Boyer
- Graduate Group in Human Development, University of California, Davis, Davis, CA, United States
| | - Rose Bern
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Daniella Yerumyan
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Sophia Rogers
- Graduate Group in Psychology, University of California, Davis, Davis, CA, United States
| | - Sabrina L. Mederos
- Graduate Group in Animal Behavior, University of California, Davis, Davis, CA, United States
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15
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Zhang C, Wang Z, Shi Y, Yu B, Song Y. Recent advances of LSD1/KDM1A inhibitors for disease therapy. Bioorg Chem 2023; 134:106443. [PMID: 36857932 DOI: 10.1016/j.bioorg.2023.106443] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/03/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) dysregulation is closely associated with the pathological processes of various diseases, especially hematologic malignancies. Significant progresses have been made in the field of LSD1-targeted drug discovery. Nine LSD1 inhibitors including tranylcypromine, ORY-1001, ORY-2001, GSK-2879552, IMG-7289, INCB059872, TAK-418, CC-90011 and SP-2577 have entered clinical stage for disease treatment as either mono- or combinational therapy. This review updates LSD1 inhibitors reported during 2022. Design strategies, structure-activity relationship studies, binding model analysis and modes of action are highlighted. In particular, the unique multiple-copies binding mode of quinazoline derivatives paves new ways for the development of reversible LSD1 inhibitors by blocking the substrate entrance. The design strategy of clinical candidate TAK-418 also provides directions for further optimization of novel irreversible LSD1 inhibitors with low hematological side effects. The influence of the stereochemistry on the potency against LSD1 and its homolog LSD2 is briefly discussed. Finally, the challenges and prospects of LSD1-targeted drug discovery are also given.
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Affiliation(s)
- Chaofeng Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhiyuan Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yuting Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Yihui Song
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
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16
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von Eyben FE, Kristiansen K, Kapp DS, Hu R, Preda O, Nogales FF. Epigenetic Regulation of Driver Genes in Testicular Tumorigenesis. Int J Mol Sci 2023; 24:ijms24044148. [PMID: 36835562 PMCID: PMC9966837 DOI: 10.3390/ijms24044148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
In testicular germ cell tumor type II (TGCT), a seminoma subtype expresses an induced pluripotent stem cell (iPSC) panel with four upregulated genes, OCT4/POU5F1, SOX17, KLF4, and MYC, and embryonal carcinoma (EC) has four upregulated genes, OCT4/POU5F1, SOX2, LIN28, and NANOG. The EC panel can reprogram cells into iPSC, and both iPSC and EC can differentiate into teratoma. This review summarizes the literature on epigenetic regulation of the genes. Epigenetic mechanisms, such as methylations of cytosines on the DNA string and methylations and acetylations of histone 3 lysines, regulate expression of these driver genes between the TGCT subtypes. In TGCT, the driver genes contribute to well-known clinical characteristics and the driver genes are also important for aggressive subtypes of many other malignancies. In conclusion, epigenetic regulation of the driver genes are important for TGCT and for oncology in general.
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Affiliation(s)
- Finn E. von Eyben
- Center for Tobacco Control Research, Birkevej 17, 5230 Odense, Denmark
- Correspondence: ; Tel.: +45-66145862
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, August Krogh Building Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark
- BGI-Research, BGI-Shenzhen, Shenzhen 518120, China
- Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 166555, China
| | - Daniel S. Kapp
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Rong Hu
- Department of Pathology, Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison, WI 53792, USA
| | - Ovidiu Preda
- Department of Pathology, San Cecilio University Hospital, 18071 Granada, CP, Spain
| | - Francisco F. Nogales
- Department of Pathology, School of Medicine, University Granada, 18071 Granada, CP, Spain
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17
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Prakasam R, Bonadiman A, Andreotti R, Zuccaro E, Dalfovo D, Marchioretti C, Tripathy D, Petris G, Anderson EN, Migazzi A, Tosatto L, Cereseto A, Battaglioli E, Sorarù G, Lim WF, Rinaldi C, Sambataro F, Pourshafie N, Grunseich C, Romanel A, Pandey UB, Contestabile A, Ronzitti G, Basso M, Pennuto M. LSD1/PRMT6-targeting gene therapy to attenuate androgen receptor toxic gain-of-function ameliorates spinobulbar muscular atrophy phenotypes in flies and mice. Nat Commun 2023; 14:603. [PMID: 36746939 PMCID: PMC9902531 DOI: 10.1038/s41467-023-36186-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
Spinobulbar muscular atrophy (SBMA) is caused by CAG expansions in the androgen receptor gene. Androgen binding to polyQ-expanded androgen receptor triggers SBMA through a combination of toxic gain-of-function and loss-of-function mechanisms. Leveraging cell lines, mice, and patient-derived specimens, we show that androgen receptor co-regulators lysine-specific demethylase 1 (LSD1) and protein arginine methyltransferase 6 (PRMT6) are overexpressed in an androgen-dependent manner specifically in the skeletal muscle of SBMA patients and mice. LSD1 and PRMT6 cooperatively and synergistically transactivate androgen receptor, and their effect is enhanced by expanded polyQ. Pharmacological and genetic silencing of LSD1 and PRMT6 attenuates polyQ-expanded androgen receptor transactivation in SBMA cells and suppresses toxicity in SBMA flies, and a preclinical approach based on miRNA-mediated silencing of LSD1 and PRMT6 attenuates disease manifestations in SBMA mice. These observations suggest that targeting overexpressed co-regulators can attenuate androgen receptor toxic gain-of-function without exacerbating loss-of-function, highlighting a potential therapeutic strategy for patients with SBMA.
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Affiliation(s)
- Ramachandran Prakasam
- Dulbecco Telethon Institute at the Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Angela Bonadiman
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Roberta Andreotti
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine, Padova, Italy
- Padova Neuroscience Center, Padova, Italy
| | - Emanuela Zuccaro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine, Padova, Italy
- Padova Neuroscience Center, Padova, Italy
| | - Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Caterina Marchioretti
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine, Padova, Italy
- Padova Neuroscience Center, Padova, Italy
| | - Debasmita Tripathy
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Gianluca Petris
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden, UK
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Alice Migazzi
- Dulbecco Telethon Institute at the Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Laura Tosatto
- Dulbecco Telethon Institute at the Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Anna Cereseto
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Elena Battaglioli
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Gianni Sorarù
- Padova Neuroscience Center, Padova, Italy
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Wooi Fang Lim
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Carlo Rinaldi
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Fabio Sambataro
- Padova Neuroscience Center, Padova, Italy
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Naemeh Pourshafie
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Christopher Grunseich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Giuseppe Ronzitti
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Evry, France
- Genethon, 91000, Evry, France
| | - Manuela Basso
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
| | - Maria Pennuto
- Dulbecco Telethon Institute at the Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
- Veneto Institute of Molecular Medicine, Padova, Italy.
- Padova Neuroscience Center, Padova, Italy.
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18
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Noce B, Di Bello E, Fioravanti R, Mai A. LSD1 inhibitors for cancer treatment: Focus on multi-target agents and compounds in clinical trials. Front Pharmacol 2023; 14:1120911. [PMID: 36817147 PMCID: PMC9932783 DOI: 10.3389/fphar.2023.1120911] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Histone lysine-specific demethylase 1 (LSD1/KDM1A) was first identified in 2004 as an epigenetic enzyme able to demethylate specific lysine residues of histone H3, namely H3K4me1/2 and H3K9me1/2, using FAD as the cofactor. It is ubiquitously overexpressed in many types of cancers (breast, gastric, prostate, hepatocellular, and esophageal cancer, acute myeloid leukemia, and others) leading to block of differentiation and increase of proliferation, migration and invasiveness at cellular level. LSD1 inhibitors can be grouped in covalent and non-covalent agents. Each group includes some hybrid compounds, able to inhibit LSD1 in addition to other target(s) at the same time (dual or multitargeting compounds). To date, 9 LSD1 inhibitors have entered clinical trials, for hematological and/or solid cancers. Seven of them (tranylcypromine, iadademstat (ORY-1001), bomedemstat (IMG-7289), GSK-2879552, INCB059872, JBI-802, and Phenelzine) covalently bind the FAD cofactor, and two are non-covalent LSD1 inhibitors [pulrodemstat (CC-90011) and seclidemstat (SP-2577)]. Another TCP-based LSD1/MAO-B dual inhibitor, vafidemstat (ORY-2001), is in clinical trial for Alzheimer's diseases and personality disorders. The present review summarizes the structure and functions of LSD1, its pathological implications in cancer and non-cancer diseases, and the identification of LSD1 covalent and non-covalent inhibitors with different chemical scaffolds, including those involved in clinical trials, highlighting their potential as potent and selective anticancer agents.
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Affiliation(s)
- Beatrice Noce
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy
| | - Elisabetta Di Bello
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy
| | - Rossella Fioravanti
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy,*Correspondence: Rossella Fioravanti,
| | - Antonello Mai
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy,Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
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19
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Song Y, Wang S, Yu B. Structural and Functional Landscape of FAD-Dependent Histone Lysine Demethylases for New Drug Discovery. J Med Chem 2023; 66:71-94. [PMID: 36537915 DOI: 10.1021/acs.jmedchem.2c01324] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Small molecules targeting the flavin adenine dinucleotide (FAD)-dependent histone lysine demethylase LSD family have displayed therapeutic promise against various diseases. Nine clinical candidates targeting the classic demethylase-dependent functions of the LSD family are currently being investigated for treating cancers, neurodegenerative diseases, etc. Moreover, targeting noncatalytic functions of LSDs also represents an emerging strategy for treating human diseases. In this Perspective, we provide full structural and functional landscape of the LSD family and action modes of different types of LSD inhibitors including natural products, peptides, and synthetic compounds, aiming to reveal new druggable space for the design of new LSD inhibitors. Particularly, we first classify these inhibitors into three types based on their unique binding modes. Additionally, the strategies targeting the demethylase-independent functions of LSDs are also briefly discussed. This Perspective may benefit the discovery of new LSD inhibitors for probing LSD biology and/or treating human diseases.
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Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shu Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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20
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Hu R, Hameed UFS, Sun X, Moorthy BS, Zhang W, Jeffrey PD, Zhou L, Ma X, Chen F, Pei J, Giri PK, Mou Y, Swaminathan K, Yuan P. A NR2E1-interacting peptide of LSD1 inhibits the proliferation of brain tumour initiating cells. Cell Prolif 2023; 56:e13350. [PMID: 36321378 DOI: 10.1111/cpr.13350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVES Elimination of brain tumour initiating cells (BTICs) is important for the good prognosis of malignant brain tumour treatment. To develop a novel strategy targeting BTICs, we studied NR2E1(TLX) involved self-renewal mechanism of BTICs and explored the intervention means. MATERIALS AND METHODS NR2E1 and its interacting protein-LSD1 in BTICs were studied by gene interference combined with cell growth, tumour sphere formation, co-immunoprecipitation and chromatin immunoprecipitation assays. NR2E1 interacting peptide of LSD1 was identified by Amide Hydrogen/Deuterium Exchange and Mass Spectrometry (HDX-MS) and analysed by in vitro functional assays. The in vivo function of the peptide was examined with intracranial mouse model by transplanting patient-derived BTICs. RESULTS We found NR2E1 recruits LSD1, a lysine demethylase, to demethylate mono- and di-methylated histone 3 Lys4 (H3K4me/me2) at the Pten promoter and repress its expression, thereby promoting BTIC proliferation. Using Amide Hydrogen/Deuterium Exchange and Mass Spectrometry (HDX-MS) method, we identified four LSD1 peptides that may interact with NR2E1. One of the peptides, LSD1-197-211 that locates at the LSD1 SWIRM domain, strongly inhibited BTIC proliferation by promoting Pten expression through interfering NR2E1 and LSD1 function. Furthermore, overexpression of this peptide in human BTICs can inhibit intracranial tumour formation. CONCLUSION Peptide LSD1-197-211 can repress BTICs by interfering the synergistic function of NR2E1 and LSD1 and may be a promising lead peptide for brain tumour therapy in future.
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Affiliation(s)
- Rong Hu
- Guangdong Institute of Gastroenterology, Guangzhou, People's Republic of China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | - Xiang Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | | | - Wen Zhang
- Guangdong Institute of Gastroenterology, Guangzhou, People's Republic of China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Li Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xin Ma
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fangjin Chen
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Pankaj K Giri
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Yonggao Mou
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | | | - Ping Yuan
- Guangdong Institute of Gastroenterology, Guangzhou, People's Republic of China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
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21
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Mao F, Shi YG. Targeting the LSD1/KDM1 Family of Lysine Demethylases in Cancer and Other Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:15-49. [PMID: 37751134 DOI: 10.1007/978-3-031-38176-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) was the first histone demethylase discovered and the founding member of the flavin-dependent lysine demethylase family (KDM1). The human KDM1 family includes KDM1A and KDM1B, which primarily catalyze demethylation of histone H3K4me1/2. The KDM1 family is involved in epigenetic gene regulation and plays important roles in various biological and disease pathogenesis processes, including cell differentiation, embryonic development, hormone signaling, and carcinogenesis. Malfunction of many epigenetic regulators results in complex human diseases, including cancers. Regulators such as KDM1 have become potential therapeutic targets because of the reversibility of epigenetic control of genome function. Indeed, several classes of KDM1-selective small molecule inhibitors have been developed, some of which are currently in clinical trials to treat various cancers. In this chapter, we review the discovery, biochemical, and molecular mechanisms, atomic structure, genetics, biology, and pathology of the KDM1 family of lysine demethylases. Focusing on cancer, we also provide a comprehensive summary of recently developed KDM1 inhibitors and related preclinical and clinical studies to provide a better understanding of the mechanisms of action and applications of these KDM1-specific inhibitors in therapeutic treatment.
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Affiliation(s)
- Fei Mao
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yujiang Geno Shi
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China.
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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22
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Yang GJ, Liu YJ, Ding LJ, Tao F, Zhu MH, Shi ZY, Wen JM, Niu MY, Li X, Xu ZS, Qin WJ, Fei CJ, Chen J. A state-of-the-art review on LSD1 and its inhibitors in breast cancer: Molecular mechanisms and therapeutic significance. Front Pharmacol 2022; 13:989575. [PMID: 36188536 PMCID: PMC9523086 DOI: 10.3389/fphar.2022.989575] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer (BC) is a kind of malignant cancer in women, and it has become the most diagnosed cancer worldwide since 2020. Histone methylation is a common biological epigenetic modification mediating varieties of physiological and pathological processes. Lysine-specific demethylase 1 (LSD1), a first identified histone demethylase, mediates the removal of methyl groups from histones H3K4me1/2 and H3K9me1/2 and plays a crucial role in varieties of cancer progression. It is also specifically amplified in breast cancer and contributes to BC tumorigenesis and drug resistance via both demethylase and non-demethylase manners. This review will provide insight into the overview structure of LSD1, summarize its action mechanisms in BC, describe the therapeutic potential of LSD1 inhibitors in BC, and prospect the current opportunities and challenges of targeting LSD1 for BC therapy.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
| | - Yan-Jun Liu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Li-Jian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Fan Tao
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Ming-Hui Zhu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhen-Yuan Shi
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Juan-Ming Wen
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Meng-Yao Niu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xiang Li
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhan-Song Xu
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wan-Jia Qin
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Chen-Jie Fei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, China
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23
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Wang MM, Nguyen TVT, Waser J. Activation of aminocyclopropanes via radical intermediates. Chem Soc Rev 2022; 51:7344-7357. [PMID: 35938356 DOI: 10.1039/d2cs00090c] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aminocyclopropanes are versatile building blocks for accessing high value-added nitrogen-containing products. To control ring-opening promoted by ring strain, the Lewis acid activation of donor-acceptor substituted systems is now well established. Over the last decade, alternative approaches have emerged proceeding via the formation of radical intermediates, alleviating the need for double activation of the cyclopropanes. This tutorial review summarizes key concepts and recent progress in ring-opening transformations of aminocyclopropanes via radical intermediates, divided into formal cycloadditions and 1,3-difunctionalizations.
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Affiliation(s)
- Ming-Ming Wang
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. .,Department of Chemical Biology, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Tin V T Nguyen
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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24
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Takada Y, Yamashita Y, Itoh Y, Suzuki T. Medicinal Chemistry Research on Targeting Epigenetic Complexes. J SYN ORG CHEM JPN 2022. [DOI: 10.5059/yukigoseikyokaishi.80.664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Bou-Fakhredin R, De Franceschi L, Motta I, Cappellini MD, Taher AT. Pharmacological Induction of Fetal Hemoglobin in β-Thalassemia and Sickle Cell Disease: An Updated Perspective. Pharmaceuticals (Basel) 2022; 15:ph15060753. [PMID: 35745672 PMCID: PMC9227505 DOI: 10.3390/ph15060753] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
A significant amount of attention has recently been devoted to the mechanisms involved in hemoglobin (Hb) switching, as it has previously been established that the induction of fetal hemoglobin (HbF) production in significant amounts can reduce the severity of the clinical course in diseases such as β-thalassemia and sickle cell disease (SCD). While the induction of HbF using lentiviral and genome-editing strategies has been made possible, they present limitations. Meanwhile, progress in the use of pharmacologic agents for HbF induction and the identification of novel HbF-inducing strategies has been made possible as a result of a better understanding of γ-globin regulation. In this review, we will provide an update on all current pharmacological inducer agents of HbF in β-thalassemia and SCD in addition to the ongoing research into other novel, and potentially therapeutic, HbF-inducing agents.
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Affiliation(s)
- Rayan Bou-Fakhredin
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (R.B.-F.); (I.M.)
| | - Lucia De Franceschi
- Department of Medicine, University of Verona and Azienda Ospedaliera Universitaria Verona, 37128 Verona, Italy;
| | - Irene Motta
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (R.B.-F.); (I.M.)
- UOC General Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (R.B.-F.); (I.M.)
- UOC General Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Correspondence: (M.D.C.); (A.T.T.)
| | - Ali T. Taher
- Department of Internal Medicine, Division of Hematology-Oncology, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon
- Correspondence: (M.D.C.); (A.T.T.)
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26
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Koda Y, Sato S, Yamamoto H, Niwa H, Watanabe H, Watanabe C, Sato T, Nakamura K, Tanaka A, Shirouzu M, Honma T, Fukami T, Koyama H, Umehara T. Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles. ACS Med Chem Lett 2022; 13:848-854. [PMID: 35586426 PMCID: PMC9109268 DOI: 10.1021/acsmedchemlett.2c00120] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/21/2022] [Indexed: 12/26/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) is a promising therapeutic target for the treatment of cancers. Several derivatives of tranylcypromine (trans-2-phenylcyclopropylamine) have been developed as LSD1 inhibitors. One such derivative is S2157; however, this compound has a high hERG channel inhibitory activity and a low microsomal stability, making it unsuitable as a drug candidate. Here, using an in silico hERG inhibition prediction model, we designed, synthesized, and evaluated a novel series of S2157 derivatives characterized by modifications of the benzyloxy and piperazine groups. Among the synthesized derivatives, a compound possessing 2-fluoropyridine and 2,8-diaza-spiro[4.5]decane groups (compound 10) showed the most desirable activities, and its eutomer, S1427, was isolated by the optical resolution of 10. In addition to potent LSD1 inhibitory activity, S1427 exhibited desirable hERG channel inhibition and microsomal stability profiles.
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Affiliation(s)
- Yasuko Koda
- Drug Discovery Chemistry Platform Unit, Drug Discovery Seed Compounds Exploratory Unit, Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shin Sato
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hirofumi Yamamoto
- Drug Discovery Chemistry Platform Unit, Drug Discovery Seed Compounds Exploratory Unit, Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hideaki Niwa
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hisami Watanabe
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chiduru Watanabe
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Tomohiro Sato
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kana Nakamura
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Tanaka
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takehiro Fukami
- RIKEN Program for Drug Discovery and Medical Technology Platforms, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroo Koyama
- Drug Discovery Chemistry Platform Unit, Drug Discovery Seed Compounds Exploratory Unit, Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamic Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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27
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Tang D, He J, Dai Y, Geng X, Leng Q, Jiang H, Sun R, Xu S. Targeting KDM1B-dependent miR-215-AR-AGR2-axis promotes sensitivity to enzalutamide-resistant prostate cancer. Cancer Gene Ther 2022; 29:543-557. [PMID: 33854217 DOI: 10.1038/s41417-021-00332-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/07/2021] [Accepted: 03/24/2021] [Indexed: 02/02/2023]
Abstract
Post-translational modifications of histones by histone demethylases plays an important role in the regulation of gene transcription and are implicated in cancers. Castrate resistant prostate cancer (CRPC) is often driven by constitutively active androgen receptor and commonly becomes resistant to established hormonal therapy strategies such as enzalutamide as a result. However, the role of KDM1B involved in next generation anti-enzalutamide resistance and the mechanisms of KDM1B regulation are poorly defined. Here, we show that KDM1B is upregulated and correlated with prostate cancer progression and poor prognosis. Downregulation of miR-215 is correlated with overexpression of KDM1B in enzalutamide-resistant prostate cancer cells, which promotes AR-dependent AGR2 transcription and regulates the sensitivity to next generation AR-targeted therapy. Inhibition of KDM1B significantly inhibits prostate tumor growth and improves enzalutamide treatments through AGR2 suppression. Our studies demonstrate inhibition of KDM1B can offer a viable therapeutic option to overcome enzalutamide resistance in tumors with deregulated miR-215-KDM1B-AR-AGR2 signaling axis.
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Affiliation(s)
- Donge Tang
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong, China
| | - Jiaxi He
- Department of Pathology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yong Dai
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong, China
| | - Xinyan Geng
- Department of Biochemistry, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Qixin Leng
- Department of Pathology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Haowu Jiang
- Department of Anesthesiology and Center for the Study of Itch, Washington University School of Medicine, St. Louis, MO, USA
| | - Rui Sun
- Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Songhui Xu
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
- Department of Pathology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
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28
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Kamerzell TJ, Mikell B, Chen L, Elias H, Dawn B, MacRae C, Middaugh CR. The structural basis of histone modifying enzyme specificity and promiscuity: Implications for metabolic regulation and drug design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:189-243. [PMID: 35534108 DOI: 10.1016/bs.apcsb.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Histone modifying enzymes regulate chromatin architecture through covalent modifications and ultimately control multiple aspects of cellular function. Disruption of histone modification leads to changes in gene expression profiles and may lead to disease. Both small molecule inhibitors and intermediary metabolites have been shown to modulate histone modifying enzyme activity although our ability to identify successful drug candidates or novel metabolic regulators of these enzymes has been limited. Using a combination of large scale in silico screens and in vivo phenotypic analysis, we identified several small molecules and intermediary metabolites with distinctive HME activity. Our approach using unsupervised learning identifies the chemical fingerprints of both small molecules and metabolites that facilitate recognition by the enzymes active sites which can be used as a blueprint to design novel inhibitors. Furthermore, this work supports the idea that histone modifying enzymes sense intermediary metabolites integrating genes, environment and cellular physiology.
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Affiliation(s)
- Tim J Kamerzell
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States; Division of Internal Medicine, HCA MidWest Health, Overland Park, KS, United States; Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States; Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States; Applied AI Technologies, LLC, Overland Park, KS, United States.
| | - Brittney Mikell
- Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Lei Chen
- Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Harold Elias
- Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Buddhadeb Dawn
- Division of Cardiovascular Diseases, Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Calum MacRae
- Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
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29
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Nicosia L, Boffo FL, Ceccacci E, Conforti F, Pallavicini I, Bedin F, Ravasio R, Massignani E, Somervaille TCP, Minucci S, Bonaldi T. Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1 oncogenic functions in AML. Oncogene 2022; 41:878-894. [PMID: 34862459 PMCID: PMC8830420 DOI: 10.1038/s41388-021-02123-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 12/19/2022]
Abstract
The histone demethylase LSD1 is over-expressed in hematological tumors and has emerged as a promising target for anticancer treatment, so that several LSD1 inhibitors are under development and testing, in preclinical and clinical settings. However, the complete understanding of their complex mechanism of action is still unreached. Here, we unraveled a novel mode of action of the LSD1 inhibitors MC2580 and DDP-38003, showing that they can induce differentiation of AML cells through the downregulation of the chromatin protein GSE1. Analysis of the phenotypic effects of GSE1 depletion in NB4 cells showed a strong decrease of cell viability in vitro and of tumor growth in vivo. Mechanistically, we found that a set of genes associated with immune response and cytokine-signaling pathways are upregulated by LSD1 inhibitors through GSE1-protein reduction and that LSD1 and GSE1 colocalize at promoters of a subset of these genes at the basal state, enforcing their transcriptional silencing. Moreover, we show that LSD1 inhibitors lead to the reduced binding of GSE1 to these promoters, activating transcriptional programs that trigger myeloid differentiation. Our study offers new insights into GSE1 as a novel therapeutic target for AML.
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Affiliation(s)
- Luciano Nicosia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Oglesby Cancer Research Centre Building, Manchester, M20 4GJ, UK
| | - Francesca Ludovica Boffo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Elena Ceccacci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Fabio Conforti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Isabella Pallavicini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Roberto Ravasio
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy
| | - Tim C P Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Oglesby Cancer Research Centre Building, Manchester, M20 4GJ, UK
| | - Saverio Minucci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy
- Department of Biosciences, University of Milan, Milan, 20133, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20139, Italy.
- Department of Oncology and Haemato-Oncology, University of Milan, Milan, 20133, Italy.
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30
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Du Y, Zhang Y, Huang M, Wang S, Wang J, Liao K, Wu X, Zhou Q, Zhang X, Wu YD, Peng T. Systematic investigation of the aza-Cope reaction for fluorescence imaging of formaldehyde in vitro and in vivo. Chem Sci 2021; 12:13857-13869. [PMID: 34760171 PMCID: PMC8549814 DOI: 10.1039/d1sc04387k] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/22/2021] [Indexed: 01/02/2023] Open
Abstract
Increasing evidence has highlighted the endogenous production of formaldehyde (FA) in a variety of fundamental biological processes and its involvement in many disease conditions ranging from cancer to neurodegeneration. To examine the physiological and pathological relevance and functions of FA, fluorescent probes for FA imaging in live biological samples are of great significance. Herein we report a systematic investigation of 2-aza-Cope reactions between homoallylamines and FA for identification of a highly efficient 2-aza-Cope reaction moiety and development of fluorescent probes for imaging FA in living systems. By screening a set of N-substituted homoallylamines and comparing them to previously reported homoallylamine structures for reaction with FA, we found that N-p-methoxybenzyl homoallylamine exhibited an optimal 2-aza-Cope reactivity to FA. Theoretical calculations were then performed to demonstrate that the N-substituent on homoallylamine greatly affects the condensation with FA, which is more likely the rate-determining step. Moreover, the newly identified optimal N-p-methoxybenzyl homoallylamine moiety with a self-immolative β-elimination linker was generally utilized to construct a series of fluorescent probes with varying excitation/emission wavelengths for sensitive and selective detection of FA in aqueous solutions and live cells. Among these probes, the near-infrared probe FFP706 has been well demonstrated to enable direct fluorescence visualization of steady-state endogenous FA in live mouse brain tissues and elevated FA levels in a mouse model of breast cancer. This study provides the optimal aza-Cope reaction moiety for FA probe development and new chemical tools for fluorescence imaging and biological investigation of FA in living systems.
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Affiliation(s)
- Yimeng Du
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Yuqing Zhang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Meirong Huang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Shushu Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Jianzheng Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Kongke Liao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Xiaojun Wu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Qiang Zhou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Xinhao Zhang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
- Shenzhen Bay Laboratory Shenzhen 518132 China
| | - Yun-Dong Wu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
- Shenzhen Bay Laboratory Shenzhen 518132 China
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
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The Molecular Biology of Susceptibility to Post-Traumatic Stress Disorder: Highlights of Epigenetics and Epigenomics. Int J Mol Sci 2021; 22:ijms221910743. [PMID: 34639084 PMCID: PMC8509551 DOI: 10.3390/ijms221910743] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
Exposure to trauma is one of the most important and prevalent risk factors for mental and physical ill-health. Excessive or prolonged stress exposure increases the risk of a wide variety of mental and physical symptoms. However, people differ strikingly in their susceptibility to develop signs and symptoms of mental illness after traumatic stress. Post-traumatic stress disorder (PTSD) is a debilitating disorder affecting approximately 8% of the world’s population during their lifetime, and typically develops after exposure to a traumatic event. Despite that exposure to potentially traumatizing events occurs in a large proportion of the general population, about 80–90% of trauma-exposed individuals do not develop PTSD, suggesting an inter-individual difference in vulnerability to PTSD. While the biological mechanisms underlying this differential susceptibility are unknown, epigenetic changes have been proposed to underlie the relationship between exposure to traumatic stress and the susceptibility to develop PTSD. Epigenetic mechanisms refer to environmentally sensitive modifications to DNA and RNA molecules that regulate gene transcription without altering the genetic sequence itself. In this review, we provide an overview of various molecular biological, biochemical and physiological alterations in PTSD, focusing on changes at the genomic and epigenomic level. Finally, we will discuss how current knowledge may aid us in early detection and improved management of PTSD patients.
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Naillat F, Saadeh H, Nowacka-Woszuk J, Gahurova L, Santos F, Tomizawa SI, Kelsey G. Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes. Clin Epigenetics 2021; 13:132. [PMID: 34183052 PMCID: PMC8240245 DOI: 10.1186/s13148-021-01116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. Such techniques are used routinely in both rodent and human species. DNA methylation is a dynamic process that plays a role in epigenetic regulation of gametogenesis and development. In mammalian oocytes, DNA methylation establishment regulates gene expression in the embryos. This regulation is particularly important for a class of genes, imprinted genes, whose expression patterns are crucial for the next generation. The aim of this work was to establish an in vitro culture system for immature mouse oocytes that will allow manipulation of specific factors for a deeper analysis of regulatory mechanisms for establishing transcription regulation-associated methylation patterns. RESULTS An in vitro culture system was developed from immature mouse oocytes that were grown to germinal vesicles (GV) under two different conditions: normoxia (20% oxygen, 20% O2) and hypoxia (5% oxygen, 5% O2). The cultured oocytes were sorted based on their sizes. Reduced representative bisulphite sequencing (RRBS) and RNA-seq libraries were generated from cultured and compared to in vivo-grown oocytes. In the in vitro cultured oocytes, global and CpG-island (CGI) methylation increased gradually along with oocyte growth, and methylation of the imprinted genes was similar to in vivo-grown oocytes. Transcriptomes of the oocytes grown in normoxia revealed chromatin reorganisation and enriched expression of female reproductive genes, whereas in the 5% O2 condition, transcripts were biased towards cellular stress responses. To further confirm the results, we developed a functional assay based on our model for characterising oocyte methylation using drugs that reduce methylation and transcription. When histone methylation and transcription processes were reduced, DNA methylation at CGIs from gene bodies of grown oocytes presented a lower methylation profile. CONCLUSIONS Our observations reveal changes in DNA methylation and transcripts between oocytes cultured in vitro with different oxygen concentrations and in vivo-grown murine oocytes. Oocytes grown under 20% O2 had a higher correlation with in vivo oocytes for DNA methylation and transcription demonstrating that higher oxygen concentration is beneficial for the oocyte maturation in ex vivo culture condition. Our results shed light on epigenetic mechanisms for the development of oocytes from an immature to GV oocyte in an in vitro culture model.
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Affiliation(s)
- Florence Naillat
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Diseases Network Research Unit, Faculty of Biochemistry and Molecular Medicine, Oulu University, Oulu, Finland.
| | - Heba Saadeh
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Computer Science, King Abdullah II School of Information Technology, The University of Jordan, Amman, Jordan
| | - Joanna Nowacka-Woszuk
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Lenka Gahurova
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Laboratory of Early Mammalian Development, Department of Molecular Biology and Genetics, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Fatima Santos
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Shin-Ichi Tomizawa
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,School of Medicine, Yokohama City University, Yokohama, Japan
| | - Gavin Kelsey
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
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Lysine-specific demethylase 1A restricts ex vivo propagation of human HSCs and is a target of UM171. Blood 2021; 136:2151-2161. [PMID: 32582923 DOI: 10.1182/blood.2020005827] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/07/2020] [Indexed: 12/23/2022] Open
Abstract
Culture conditions in which hematopoietic stem cells (HSCs) can be expanded for clinical benefit are highly sought after. Here, we report that inhibition of the epigenetic regulator lysine-specific histone demethylase 1A (LSD1) induces a rapid expansion of human cord blood-derived CD34+ cells and promotes in vitro propagation of long-term repopulating HSCs by preventing differentiation. The phenotype and molecular characteristics of cells treated with LSD1 inhibitors were highly similar to cells treated with UM171, an agent promoting expansion of HSCs through undefined mechanisms and currently being tested in clinical trials. Strikingly, we found that LSD1, as well as other members of the LSD1-containing chromatin remodeling complex CoREST, is rapidly polyubiquitinated and degraded upon UM171 treatment. CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 depletion of the CoREST core member, RCOR1, resulted in expansion of CD34+ cells similar to LSD1 inhibition and UM171. Taken together, LSD1 and CoREST restrict HSC expansion and are principal targets of UM171, forming a mechanistic basis for the HSC-promoting activity of UM171.
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34
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Zhang Y, Rong D, Li B, Wang Y. Targeting Epigenetic Regulators with Covalent Small-Molecule Inhibitors. J Med Chem 2021; 64:7900-7925. [PMID: 33599482 DOI: 10.1021/acs.jmedchem.0c02055] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic regulation of gene expression plays a critical role in various physiological processes, and epigenetic dysregulation is implicated in a number of diseases, prominently including cancer. Epigenetic regulators have been validated as potential therapeutic targets, and significant progress has been made in the discovery and development of epigenetic-based inhibitors. However, successful epigenetic drug discovery is still facing challenges, including moderate selectivity, limited efficacy, and acquired drug resistance. Inspired by the advantages of covalent small-molecule inhibitors, targeted covalent inhibition has attracted increasing interest in epigenetic drug discovery. In this review, we comprehensively summarize the structure-based design and characterization of covalent inhibitors targeting epigenetic writers, readers, and erasers and highlight their potential benefits in enhancing selectivity across the enzyme family and improving in vivo efficacy. We also discuss the challenges and opportunities of covalent small-molecule inhibitors and hope to shed light on future epigenetic drug discovery.
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Affiliation(s)
- Yi Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Deqin Rong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bingbing Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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35
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Cui J, Zhang Y, Ren X, Jin L, Zhang H. TBX1 Functions as a Tumor Activator in Prostate Cancer by Promoting Ribosome RNA Gene Transcription. Front Oncol 2021; 10:616173. [PMID: 33575219 PMCID: PMC7871003 DOI: 10.3389/fonc.2020.616173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/14/2020] [Indexed: 11/20/2022] Open
Abstract
TBX1 belongs to an evolutionarily conserved family of transcription factors involved in organ development. TBX1 has been reported to have a hypermethylated cytosine guanine dinucleotide island around its second exon, which was related to prostate cancer (PCa) progression. However, the role and exact mechanism of TBX1 in PCa remains unknown. Using human prostate samples, online data mining and multiple in vitro and in vivo models, we examined the biological role and underlying mechanisms of TBX1 in PCa. TBX1 was highly expressed in PCa tissues, and high TBX1 expression was positively associated with Gleason score, pathological tumor stage, pathological lymph node stage, extraprostatic extension and disease/progression-free survival. In vitro and in vivo data demonstrated that TBX1 silencing inhibits PCa cell proliferation and colony formation and increases the cell population at the G0/G1 phase. The exogenous expression of TBX1 rescued these phenotypes. Mechanistically, TBX1 silencing suppressed the expression of 45S ribosomal RNA (rRNA), which was rescued by the exogenous expression of TBX1. TBX1 silencing inhibited the monomethylation of histone 3 lysine 4 (H3K4me1) binding with the non-coding intergenic spacer (IGS) regions of ribosomal DNA (rDNA) and the recruitment of upstream binding factor to the promoter and IGS regions of rDNA. The drug-induced enhancement of H3K4me1 counteracted the effect of TBX1 silencing. These findings indicate that TBX1 exerts its tumor activator function in PCa cells via epigenetic control, thereby promoting rRNA gene transcription. Thus, TBX1 may represent a prognostic biomarker and therapeutic target for PCa patients.
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Affiliation(s)
- Jie Cui
- Department of Oncology, The First Affiliated Hospital, Xi'an Medical University, Xi'an, China.,School of General Medicine, Xi'an Medical University, Xi'an, China
| | - Yamin Zhang
- Department of Oncology, The First Affiliated Hospital, Xi'an Medical University, Xi'an, China.,School of General Medicine, Xi'an Medical University, Xi'an, China
| | - Xiaoyue Ren
- Department of Oncology, The First Affiliated Hospital, Xi'an Medical University, Xi'an, China.,School of General Medicine, Xi'an Medical University, Xi'an, China
| | - Lei Jin
- School of General Medicine, Xi'an Medical University, Xi'an, China
| | - Hongyi Zhang
- School of General Medicine, Xi'an Medical University, Xi'an, China.,Department of Urology, The First Affiliated Hospital, Xi'an Medical University, Xi'an, China
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Sun Y, Li N, Su M, Wang X, Zhao D, Xiong B, Zhou Y, Liu T, Chen YL. Divalent tranylcypromine derivative as lysine-specific demethylase 1 inhibitor. Med Chem Res 2021. [DOI: 10.1007/s00044-020-02689-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Karakousis ND, Papatheodoridi A, Chatzigeorgiou A, Papatheodoridis G. Cellular senescence and hepatitis B-related hepatocellular carcinoma: An intriguing link. Liver Int 2020; 40:2917-2927. [PMID: 32890439 DOI: 10.1111/liv.14659] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 02/06/2023]
Abstract
Chronic hepatitis B is mainly responsible for the morbidity and mortality from hepatitis B virus (HBV)-related complications, including hepatocellular carcinoma (HCC) and decompensated cirrhosis. Hepatocellular carcinoma remains the main challenge in the management of not only undiagnosed and/or untreated but also diagnosed and treated patients with chronic HBV infection, as its incidence decreases but is not eliminated even after many years of effective anti-HBV therapy. The exact mechanisms used by HBV to cause malignant transformation remain uncertain, although much of the available data are in favour of a pathogenetic role of HBx protein. Senescence is a cellular state, in which cells lose their ability to proliferate. This biological mechanism may function in a dual mode, namely being both cancer-protective as a result of reduced cellular proliferation, but also cancer-enhancing as a result of modulation of the tissular microenvironment by immune cells during persistent accumulation of senescent cells. Protein X of HBV protein exhibits many similarities in terms of the implemented mechanisms of action and pathways related to the biological process of cellular senescence. Concurrently, insufficient clearance of both senescent and precancerous hepatocytes combined with inadequate immune surveillance as a result of immunosenescence caused by chronic HBV infection may lead to hepatocarcinogenesis. Thus, the effect of HBV seems to be critical as a connecting link between cellular senescence and development of HCC. An ongoing research is underway towards identifying and validating markers of hepatocyte senescence, which could improve the landscape for evaluation of chronic liver disease, thereby providing valuable information in terms of HBV-related carcinogenesis.
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Affiliation(s)
- Nikolaos D Karakousis
- Department of Gastroenterology, Medical School of National and Kapodistrian University of Athens, General Hospital of Athens "Laiko", Athens, Greece.,Department of Physiology, Medical School of National and Kapodistrian University of Athens, Athens, Greece
| | - Alkistis Papatheodoridi
- Department of Physiology, Medical School of National and Kapodistrian University of Athens, Athens, Greece.,Department of Clinical Therapeutics, Medical School of National and Kapodistrian University of Athens, "Alexandra" General Hospital of Athens, Athens, Greece
| | - Antonios Chatzigeorgiou
- Department of Physiology, Medical School of National and Kapodistrian University of Athens, Athens, Greece.,Institute for Clinical Chemistry and Laboratory Medicine, University Clinic Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - George Papatheodoridis
- Department of Gastroenterology, Medical School of National and Kapodistrian University of Athens, General Hospital of Athens "Laiko", Athens, Greece
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38
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The circadian machinery links metabolic disorders and depression: A review of pathways, proteins and potential pharmacological interventions. Life Sci 2020; 265:118809. [PMID: 33249097 DOI: 10.1016/j.lfs.2020.118809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
Circadian rhythms are responsible for regulating a number of physiological processes. The central oscillator is located within the suprachiasmatic nucleus (SCN) of the hypothalamus and the SCN synchronises the circadian clocks that are found in our peripheral organs through neural and humoral signalling. At the molecular level, biological clocks consist of transcription-translation feedback loops (TTFLs) and these pathways are influenced by transcription factors, post-translational modifications, signalling pathways and epigenetic modifiers. When disruptions occur in the circadian machinery, the activities of the proteins implicated in this network and the expression of core clock or clock-controlled genes (CCGs) can be altered. Circadian misalignment can also arise when there is desychronisation between our internal clocks and environmental stimuli. There is evidence in the literature demonstrating that disturbances in the circadian rhythm contribute to the pathophysiology of several diseases and disorders. This includes the metabolic syndrome and recently, it has been suggested that the 'circadian syndrome' may be a more appropriate term to use to not only describe the cardio-metabolic risk factors but also the associated comorbidities. Here we overview the molecular architecture of circadian clocks in mammals and provide insight into the effects of shift work, exposure to artificial light, food intake and stress on the circadian rhythm. The relationship between circadian rhythms, metabolic disorders and depression is reviewed and this is a topic that requires further investigation. We also describe how particular proteins involved in the TTFLs can be potentially modulated by small molecules, including pharmacological interventions and dietary compounds.
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39
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Hoyer-Fender S. Transgenerational effect of drug-mediated inhibition of LSD1 on eye pigment expression in Drosophila. BMC Ecol 2020; 20:62. [PMID: 33228645 PMCID: PMC7684728 DOI: 10.1186/s12898-020-00330-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 11/11/2020] [Indexed: 11/25/2022] Open
Abstract
Background The Drosophila melanogaster mutant white-mottled is a well-established model for position-effect variegation (PEV). Transposition of the euchromatic white gene into the vicinity of the pericentric heterochromatin caused variegated expression of white due to heterochromatin spreading. The establishment of the euchromatin-heterochromatin boundary and spreading of silencing is regulated by mutually exclusive histone modifications, i.e. the methylations of histone H3 at lysine 9 and lysine 4. Demethylation of H3K4, catalysed by lysine-specific demethylase LSD1, is required for subsequent methylation of H3K9 to establish heterochromatin. LSD1 is therefore essential for heterochromatin formation and spreading. We asked whether drug-mediated inhibition of LSD affects the expression of white and if this induced change can be transmitted to those generations that have never been exposed to the triggering signal, i.e. transgenerational epigenetic inheritance. Results We used the lysine-specific demethylase 1 (LSD1)-inhibitor Tranylcypromine to investigate its effect on eye colour expression in consecutive generations by feeding the parental and F1 generations of the Drosophila melanogaster mutant white-mottled. Quantitative Western blotting revealed that Tranylcypromine inhibits H3K4-demethylation both in vitro in S2 cells as well as in embryos when used as feeding additive. Eye colour expression in male flies was determined by optical measurement of pigment extracts and qRT-PCR of white gene expression. Flies raised in the presence of Tranylcypromine and its solvent DMSO showed increased eye pigment expression. Beyond that, eye pigment expression was also affected in consecutive generations including F3, which is the first generation without contact with the inhibitor. Conclusions Our results show that feeding of Tranylcypromine and DMSO caused desilencing of white in treated flies of generation F1. Consecutive generations, raised on standard food without further supplements, are also affected by the drug-induced alteration of histone modifications. Although eye pigment expression eventually returned to the basal state, the observed long-lasting effect points to a memory capacity of previous epigenomes. Furthermore, our results indicate that food compounds potentially affect chromatin modification and hence gene expression and that the alteration is putatively inherited not only parentally but transgenerationally.
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Affiliation(s)
- Sigrid Hoyer-Fender
- Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology-Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, Göttingen, Germany.
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40
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Montalvo-Casimiro M, González-Barrios R, Meraz-Rodriguez MA, Juárez-González VT, Arriaga-Canon C, Herrera LA. Epidrug Repurposing: Discovering New Faces of Old Acquaintances in Cancer Therapy. Front Oncol 2020; 10:605386. [PMID: 33312959 PMCID: PMC7708379 DOI: 10.3389/fonc.2020.605386] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Gene mutations are strongly associated with tumor progression and are well known in cancer development. However, recently discovered epigenetic alterations have shown the potential to greatly influence tumoral response to therapy regimens. Such epigenetic alterations have proven to be dynamic, and thus could be restored. Due to their reversible nature, the promising opportunity to improve chemotherapy response using epigenetic therapy has arisen. Beyond helping to understand the biology of the disease, the use of modern clinical epigenetics is being incorporated into the management of the cancer patient. Potential epidrug candidates can be found through a process known as drug repositioning or repurposing, a promising strategy for the discovery of novel potential targets in already approved drugs. At present, novel epidrug candidates have been identified in preclinical studies and some others are currently being tested in clinical trials, ready to be repositioned. This epidrug repurposing could circumvent the classic paradigm where the main focus is the development of agents with one indication only, while giving patients lower cost therapies and a novel precision medical approach to optimize treatment efficacy and reduce toxicity. This review focuses on the main approved epidrugs, and their druggable targets, that are currently being used in cancer therapy. Also, we highlight the importance of epidrug repurposing by the rediscovery of known chemical entities that may enhance epigenetic therapy in cancer, contributing to the development of precision medicine in oncology.
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Affiliation(s)
- Michel Montalvo-Casimiro
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Marco Antonio Meraz-Rodriguez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | | | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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41
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Yang Y, Hu J, Fang H, Hou X, Hou Z, Sang L, Yang X. Enantioseparation of lysine derivatives on amylose tris (3, 5-dimethylphenylcarbamate) as chiral stationary phase with high separation factor. J Chromatogr A 2020; 1632:461598. [DOI: 10.1016/j.chroma.2020.461598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/03/2020] [Accepted: 09/28/2020] [Indexed: 01/10/2023]
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42
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Blokhin IO, Khorkova O, Saveanu RV, Wahlestedt C. Molecular mechanisms of psychiatric diseases. Neurobiol Dis 2020; 146:105136. [PMID: 33080337 DOI: 10.1016/j.nbd.2020.105136] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/24/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
For most psychiatric diseases, pathogenetic concepts as well as paradigms underlying neuropsychopharmacologic approaches currently revolve around neurotransmitters such as dopamine, serotonin, and norepinephrine. However, despite the fact that several generations of neurotransmitter-based psychotropics including atypical antipsychotics, selective serotonin reuptake inhibitors, and serotonin-norepinephrine reuptake inhibitors are available, the effectiveness of these medications is limited, and relapse rates in psychiatric diseases are relatively high, indicating potential involvement of other pathogenetic pathways. Indeed, recent high-throughput studies in genetics and molecular biology have shown that pathogenesis of major psychiatric illnesses involves hundreds of genes and numerous pathways via such fundamental processes as DNA methylation, transcription, and splicing. Current review summarizes these and other molecular mechanisms of such psychiatric illnesses as schizophrenia, major depressive disorder, and alcohol use disorder and suggests a conceptual framework for future studies.
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Affiliation(s)
- Ilya O Blokhin
- Center for Therapeutic Innovation, University of Miami, Miami, FL, United States of America; Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States of America; Jackson Memorial Hospital, Miami, FL, United States of America
| | - Olga Khorkova
- OPKO Health Inc., Miami, FL, United States of America
| | - Radu V Saveanu
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States of America
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami, Miami, FL, United States of America; Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States of America.
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Jia G, Cang S, Ma P, Song Z. Capsaicin: A “hot” KDM1A/LSD1 inhibitor from peppers. Bioorg Chem 2020; 103:104161. [DOI: 10.1016/j.bioorg.2020.104161] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/30/2020] [Accepted: 08/02/2020] [Indexed: 12/18/2022]
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44
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Dai XJ, Liu Y, Xiong XP, Xue LP, Zheng YC, Liu HM. Tranylcypromine Based Lysine-Specific Demethylase 1 Inhibitor: Summary and Perspective. J Med Chem 2020; 63:14197-14215. [PMID: 32931269 DOI: 10.1021/acs.jmedchem.0c00919] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Histone lysine-specific demethylase 1 (LSD1/KDM1A) has become an important and promising anticancer target since it was first identified in 2004 and specially demethylates lysine residues of histone H3K4me1/2 and H3K9me1/2. LSD1 is ubiquitously overexpressed in diverse cancers, and abrogation of LSD1 results in inhibition of proliferation, invasion, and migration in cancer cells. Over the past decade, a number of biologically active small-molecule LSD1 inhibitors have been developed. To date, six trans-2-phenylcyclopropylamine (TCP)-based LSD1 inhibitors (including TCP, ORY-1001, GSK-2879552, INCB059872, IMG-7289, and ORY-2001) that covalently bind to the flavin adenine dinucleotide (FAD) within the LSD1 catalytic cavity have already entered into clinical trials. Here, we provide an overview about the structures, activities, and structure-activity relationship (SAR) of TCP-based LSD1 inhibitors that mainly covers the literature from 2008 to date. The opportunities, challenges, and future research directions in this emerging and promising field are also discussed.
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Affiliation(s)
- Xing-Jie Dai
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ying Liu
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xiao-Peng Xiong
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Lei-Peng Xue
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yi-Chao Zheng
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hong-Min Liu
- Key Lab of Advanced Drug Preparation Technologies, Ministry of Education of China, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
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Mehndiratta S, Liou JP. Histone lysine specific demethylase 1 inhibitors. RSC Med Chem 2020; 11:969-981. [PMID: 33479691 PMCID: PMC7513387 DOI: 10.1039/d0md00141d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
LSD1 plays a pivotal role in numerous biological functions. The overexpression of LSD1 is reported to be associated with different malignancies. Over the last decade, LSD1 has emerged as an interesting target for the treatment of acute myeloid leukaemia (AML). Numerous researchers have designed, synthesized, and evaluated various LSD1 inhibitors with diverse chemical architectures. Some of these inhibitors have entered clinical trials and are currently at different phases of clinical evaluation. This comprehensive review enlists recent research developments in LSD1 targeting pharmacophores reported over the last few years.
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Affiliation(s)
- Samir Mehndiratta
- School of Pharmacy , College of Pharmacy , Taipei Medical University , Taiwan . ; Tel: +886 2 2736 1661 ext 6130
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , Los Angeles , California , USA
| | - Jing-Ping Liou
- School of Pharmacy , College of Pharmacy , Taipei Medical University , Taiwan . ; Tel: +886 2 2736 1661 ext 6130
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Epigenomic profile and biological age. PAJAR - PAN AMERICAN JOURNAL OF AGING RESEARCH 2020. [DOI: 10.15448/2357-9641.2020.1.37125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Man ages at a constant chronological rate while their biological aging rate is extremely variable. Interventions to improve, or to slow the rate of biological aging are the subject of several research. The broad spectrum of molecules and its intricate role from the biological point of view and its relation with environmental factors are being investigated. Recently, researchers have been putting its efforts to understand the epigenetic mechanisms and how it can interfere with alterations in gene expression that leads to predisposition and, or pathological outcome. Some of these investigations have shed light about how one can determine the biological age from a simple blood sample, just by detecting the epigenetic alterations on only three CpGs sites with a reasonable certainty. Also, the enzymes inhibitors that can interfere with methylation and demethylation were effective to reverse the epigenetic mechanisms. Other studies have shown how the environmental changes since from early life can affect these alterations on the epigenome. Taking all together, some biomolecular markers are already available to determine the genetic background of an individual and this information can be used to guide the lifestyle in order to prevent some future diseases development and/or improve the quality of later life.
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Coutinho Carneiro V, de Abreu da Silva IC, Amaral MS, Pereira ASA, Silveira GO, Pires DDS, Verjovski-Almeida S, Dekker FJ, Rotili D, Mai A, Lopes-Torres EJ, Robaa D, Sippl W, Pierce RJ, Borrello MT, Ganesan A, Lancelot J, Thiengo S, Fernandez MA, Vicentino ARR, Mourão MM, Coelho FS, Fantappié MR. Pharmacological inhibition of lysine-specific demethylase 1 (LSD1) induces global transcriptional deregulation and ultrastructural alterations that impair viability in Schistosoma mansoni. PLoS Negl Trop Dis 2020; 14:e0008332. [PMID: 32609727 PMCID: PMC7329083 DOI: 10.1371/journal.pntd.0008332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
Treatment and control of schistosomiasis still rely on only one effective drug, praziquantel (PZQ) and, due to mass treatment, the increasing risk of selecting for schistosome strains that are resistant to PZQ has alerted investigators to the urgent need to develop novel therapeutic strategies. The histone-modifying enzymes (HMEs) represent promising targets for the development of epigenetic drugs against Schistosoma mansoni. In the present study, we targeted the S. mansoni lysine-specific demethylase 1 (SmLSD1), a transcriptional corepressor, using a novel and selective synthetic inhibitor, MC3935, which was used to treat schistosomula and adult worms in vitro. By using cell viability assays and optical and electron microscopy, we showed that treatment with MC3935 affected parasite motility, egg-laying, tegument, and cellular organelle structures, culminating in the death of schistosomula and adult worms. In silico molecular modeling and docking analysis suggested that MC3935 binds to the catalytic pocket of SmLSD1. Western blot analysis revealed that MC3935 inhibited SmLSD1 demethylation activity of H3K4me1/2. Knockdown of SmLSD1 by RNAi recapitulated MC3935 phenotypes in adult worms. RNA-Seq analysis of MC3935-treated parasites revealed significant differences in gene expression related to critical biological processes. Collectively, our findings show that SmLSD1 is a promising drug target for the treatment of schistosomiasis and strongly support the further development and in vivo testing of selective schistosome LSD1 inhibitors.
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Affiliation(s)
- Vitor Coutinho Carneiro
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabel Caetano de Abreu da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Adriana S. A. Pereira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Gilbert Oliveira Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | | | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan, AV Groningen, Netherlands
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Eduardo José Lopes-Torres
- Laboratório de Helmintologia Romero Lascasas Porto, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Germany
| | - Raymond J. Pierce
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Centre d’Infection et d’Immunité de Lille, Lille, France
| | - M. Teresa Borrello
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - A. Ganesan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Julien Lancelot
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Silvana Thiengo
- Laboratório de Malacologia, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Monica Ammon Fernandez
- Laboratório de Malacologia, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Amanda Roberta Revoredo Vicentino
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marina Moraes Mourão
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Fernanda Sales Coelho
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Marcelo Rosado Fantappié
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Zeng J, Li Y, Ma Z, Hu M. Advances in Small Molecules in Cellular Reprogramming: Effects, Structures, and Mechanisms. Curr Stem Cell Res Ther 2020; 16:115-132. [PMID: 32564763 DOI: 10.2174/1574888x15666200621172042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 11/22/2022]
Abstract
The method of cellular reprogramming using small molecules involves the manipulation of somatic cells to generate desired cell types under chemically limited conditions, thus avoiding the ethical controversy of embryonic stem cells and the potential hazards of gene manipulation. The combinations of small molecules and their effects on mouse and human somatic cells are similar. Several small molecules, including CHIR99021, 616452, A83-01, SB431542, forskolin, tranylcypromine and valproic acid [VPA], have been frequently used in reprogramming of mouse and human somatic cells. This indicated that the reprogramming approaches related to these compounds were essential. These approaches were mainly divided into four classes: epigenetic modification, signal modulation, metabolic modulation and senescent suppression. The structures and functions of small molecules involved in these reprogramming approaches have been studied extensively. Molecular docking gave insights into the mechanisms and structural specificities of various small molecules in the epigenetic modification. The binding modes of RG108, Bix01294, tranylcypromine and VPA with their corresponding proteins clearly illustrated the interactions between these compounds and the active sites of the proteins. Glycogen synthase kinase 3β [CHIR99021], transforming growth factor β [616452, A83-01 and SB431542] and protein kinase A [forskolin] signaling pathway play important roles in signal modulation during reprogramming, however, the mechanisms and structural specificities of these inhibitors are still unknown. Further, the numbers of small molecules in the approaches of metabolic modulation and senescent suppression were too few to compare. This review aims to serve as a reference for reprogramming through small molecules in order to benefit future regenerative medicine and clinical drug discovery.
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Affiliation(s)
- Jun Zeng
- Yunnan Key laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming 650214, China
| | - Yanjiao Li
- Yunnan Key laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming 650214, China
| | - Zhaoxia Ma
- Yunnan Key laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming 650214, China
| | - Min Hu
- Yunnan Key laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research Center, Kunming University, Kunming 650214, China
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Arifuzzaman S, Khatun MR, Khatun R. Emerging of lysine demethylases (KDMs): From pathophysiological insights to novel therapeutic opportunities. Biomed Pharmacother 2020; 129:110392. [PMID: 32574968 DOI: 10.1016/j.biopha.2020.110392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, there have been remarkable scientific advancements in the understanding of lysine demethylases (KDMs) because of their demethylation of diverse substrates, including nucleic acids and proteins. Novel structural architectures, physiological roles in the gene expression regulation, and ability to modify protein functions made KDMs the topic of interest in biomedical research. These structural diversities allow them to exert their function either alone or in complex with numerous other bio-macromolecules. Impressive number of studies have demonstrated that KDMs are localized dynamically across the cellular and tissue microenvironment. Their dysregulation is often associated with human diseases, such as cancer, immune disorders, neurological disorders, and developmental abnormalities. Advancements in the knowledge of the underlying biochemistry and disease associations have led to the development of a series of modulators and technical compounds. Given the distinct biophysical and biochemical properties of KDMs, in this review we have focused on advances related to the structure, function, disease association, and therapeutic targeting of KDMs highlighting improvements in both the specificity and efficacy of KDM modulation.
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Affiliation(s)
- Sarder Arifuzzaman
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh; Everest Pharmaceuticals Ltd., Dhaka-1208, Bangladesh.
| | - Mst Reshma Khatun
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh
| | - Rabeya Khatun
- Department of Pediatrics, TMSS Medical College and Rafatullah Community Hospital, Gokul, Bogura, 5800, Bangladesh
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50
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Wass M, Göllner S, Besenbeck B, Schlenk RF, Mundmann P, Göthert JR, Noppeney R, Schliemann C, Mikesch JH, Lenz G, Dugas M, Wermke M, Röllig C, Bornhäuser M, Serve H, Platzbecker U, Foerster KI, Burhenne J, Haefeli WE, Müller LP, Binder M, Pabst C, Müller-Tidow C. A proof of concept phase I/II pilot trial of LSD1 inhibition by tranylcypromine combined with ATRA in refractory/relapsed AML patients not eligible for intensive therapy. Leukemia 2020; 35:701-711. [PMID: 32561840 PMCID: PMC7303943 DOI: 10.1038/s41375-020-0892-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 04/16/2020] [Accepted: 05/26/2020] [Indexed: 11/09/2022]
Abstract
All-trans-retinoic acid (ATRA) is highly active in acute promyelocytic leukemia but not in other types of acute myeloid leukemia (AML). Previously, we showed that ATRA in combination with Lysine-specific demethylase 1 (LSD1) inhibition by tranylcypromine (TCP) can induce myeloid differentiation in AML blasts. This phase I/II clinical trial investigated the safety and efficacy of TCP/ATRA treatment as salvage therapy for relapsed/refractory (r/r) AML. The combination was evaluated in 18 patients, ineligible for intensive treatment. The overall response rate was 20%, including two complete remissions without hematological recovery and one partial response. We also observed myeloid differentiation upon TCP/ATRA treatment in patients who did not reach clinical remission. Median overall survival (OS) was 3.3 months, and one-year OS 22%. One patient developed an ATRA-induced differentiation syndrome. The most frequently reported adverse events were vertigo and hypotension. TCP plasma levels correlated with intracellular TCP concentration. Increased H3K4me1 and H3k4me2 levels were observed in AML blasts and white blood cells from some TCP/ATRA treated patients. Combined TCP/ATRA treatment can induce differentiation of AML blasts and lead to clinical response in heavily pretreated patients with r/r AML with acceptable toxicity. These findings emphasize the potential of LSD1 inhibition combined with ATRA for AML treatment.
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Affiliation(s)
- Maxi Wass
- Department of Hematology and Oncology, University Hospital Halle, Halle (Saale), Germany.
| | - Stefanie Göllner
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Birgit Besenbeck
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Richard F Schlenk
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Petra Mundmann
- Department of Hematology and Oncology, Paracelsus-Klinik, Osnabrück, Germany
| | | | - Richard Noppeney
- Department of Hematology, University Hospital Essen, Essen, Germany
| | | | | | - Georg Lenz
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Martin Dugas
- Department of Medicine A, University Hospital Münster, Münster, Germany
| | - Martin Wermke
- Medical Clinic I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Christoph Röllig
- Medical Clinic I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Martin Bornhäuser
- Medical Clinic I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Hubert Serve
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt/Main, Germany
| | - Uwe Platzbecker
- Department of Medicine I, Hematology, Cellular Therapy, Hemostaseology, University of Leipzig, Leipzig, Germany
| | - Kathrin I Foerster
- Department of Clinical Pharmacology and Pharmacoepidemiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jürgen Burhenne
- Department of Clinical Pharmacology and Pharmacoepidemiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Walter E Haefeli
- Department of Clinical Pharmacology and Pharmacoepidemiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lutz P Müller
- Department of Hematology and Oncology, University Hospital Halle, Halle (Saale), Germany
| | - Mascha Binder
- Department of Hematology and Oncology, University Hospital Halle, Halle (Saale), Germany
| | - Caroline Pabst
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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